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Old 03-11-2011, 06:46 AM   #2
Senior Member
Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279

Check the sam header SO identifier. In the current release the sort nomenclature is not matching the SAM specification and will cause some applications the through errors. Either resort using picard, not samtools, or just use sed to modify the SO header to conform to specification
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